Peptide deformylase (PDF) has been long recognized as important in protein synthesis. Removal of the formyl moiety on methionine of nascent proteins by PDF is a necessary activity for prokaryotic cell viability (Mazel et al., Embo J (1994) 13:914-923). The central role of PDF in bacterial protein synthesis has led to significant efforts to discover antibiotics that selectively target bacterial PDFs (Howard et al., J Med Chem (2004) 47:6669-6672; Leeds and Dean Current Opinion in Pharmacology (2006) 6: 445-452). PDF inhibitors are a promising drug class, as has been demonstrated by the broad spectrum activity in vitro against drug resistant bacterial strains of the clinical drug candidates LBM415 (Watters et al., J Antimicrob Chemother (2006) 57:914-923) and BB-83698 (Lofland et al., J Antimicrob Chemother (2004) 53:664-668). The PDF inhibitor BB-83698 has been proposed as a tuberculosis treatment (Teo et al, Antimicrob Agents Chemother (2006) 50:3665-3673).
PDF activity was not believed to be important in eukaryotic cells until recently because nuclear encoded proteins are not N-formylated (Serero et al., J Biol Chem (2003) 278:52953-52963). However, in eukaryotes, mitochondrial protein synthesis involves the formylation and deformylation of proteins, as evidenced by the presence of the enzymatic machinery to perform these activities in mammals and plants, among other eukaryotes (Giglione et al., Embo J (2000). 19:5916-5929; Takeuchi et al., J Biol Chem (2001) 276:20064-20068; Takeuchi et al., J Biol Chem (1998) 273:15085-15090). The human mitochondrial Homo sapiens peptide deformylase (HsPDF) protein, which participates in the N-methionine excision pathway of newly synthesized peptides encoded by the mitochondrial genome, removes the N-terminal formyl group on the initiator methionine, and is important for cancer cell viability (Lee et al., Biochem Biophys Res Commun (2003) 312: 309-315; Lee et al., J Clin Invest (2004) 114:1107-1116; Serero et al. (2003) supra). For example, cancer cell lines appear to be more sensitive to HsPDF inhibition than normal non-cancer cell lines (Lee (2003) and Lee (2004) supra). As well, ATP depletion and mitochondrial membrane depolarization result from the inhibition of HsPDF with the PDF inhibitor actinonin. siRNA interference and pharmacologic inhibition both decrease human cell growth. Furthermore, the PDF inhibitor actinonin and its analogs exhibit anti-cancer activity in vitro and in vivo (Xu et al., Clin Cancer Res (1998) 4:171-176).
The wealth of information made available through efforts in structural genomics and advances in computation has allowed structure-based drug design to emerge as a valuable tool in medicinal chemistry. In the past combinatorial chemistry, coupled with high-throughput approaches, shifted attention away from structure-based drug discovery. Protein x-ray crystal structure determination is reversing the drug discovery process by starting with the protein crystal structure to identify and design new ligands. It is the integration of structure-based methods, virtual screening, and combinatorial chemistry that will provide the basis for more efficient drug design in the future, significantly reducing the time of the design cycle and the cost per marketed drug.